DNA polymerase



DNA polymerase (Dpo) reads a DNA strand and catalyzes the synthesis of its complementary strand. Dpo sliding clamp is made of the complex of Dpo and Proliferating Cell Nuclear Antigen (PCNA) which encircles it. The BRCT domain in Dpo is the C-terminal domain of breast cancer susceptibility protein. The Klenow fragment is a large Dpo fragment produced upon cleavage of Dpo by subtilisin. In the E. coli, the EcDpo III subunits γ, δ, δ' are named clamp loader. This complex assembles the β subunit sliding clamp unto the DNA. Rev1 is a Dpo involved in replication over DNA lesions. Terminal deoxynucleotidyl transferase (TdT) is a Dpo expressed in immature lymphoid cells. TdT adds nucleotides to exons during antibody gene recombination. The images at the left and at the right correspond to one representative Dpo, i.e. the crystal structure of DNA polymerase I from Thermus aquaticus (1taq).

3D Structures of DNA polymerase
Update June 2011

Family A – replicative and repair Dpo
2ajq – T7Dpo (mutant) + thioredoxin (mutant) + DNA - Enterobacteria phage T7

1t7p - T7Dpo (mutant) + thioredoxin + DNA

1zyq, 1x9m, 1x9s, 1x9w, 1tk0, 1skr, 1sks, 1skw, 1sl0, 1sl1, 1sl2, 1t7p - T7Dpo (mutant) + thioredoxin + DNA + nucleotide

1t8e, 1tk5, 1tk8, 1tkd - T7Dpo + thioredoxin + DNA + nucleotide

2gv9 – Dpo – Herpes simplex virus

2kzz, 1d8y, 2kzm – EcDpo I klenow fragment - Escherichia coli

1qsl - EcDpo I klenow fragment + DNA

1kfs, 1krp, 1ksp, 1kln - EcDpo I klenow fragment (mutant) + DNA

1kfd, 1dpi - EcDpo I klenow fragment + nucleotide

1d9d, 1d9f, 2kfn - EcDpo I klenow fragment + DNA + nucleotide

2kfz - EcDpo I klenow fragment (mutant) + DNA + nucleotide

1taq – TaDpo I - Thermus aquaticus

1jxe – TaDpo I Stoffel fragment

1ktq - TaDpo I klenow fragment

5ktq – TaDpo I + nucleotide

3ojs, 3oju, 1tau - TaDpo I + DNA

3m8r, 3m8s, 3lwl, 3lwm, 1qss, 1qsy, 1qtm, 2ktq, 3ktq, 4ktq - TaDpo I klenow fragment + DNA + nucleotide

1xwl - GsDpo I fragment - Geobacillus stearothermophilus

2xo7, 3hp6, 3hpo, 2hhq, 2hhs, 2hht, 2hhu, 2hhv, 2hhw, 2hhx, 2hvh, 2hvi, 2hw3, 1xc9, 1ua0, 1ua1, 1njw, 1njx, 1njy, 1njz, 1nk0, 1nk4, 1nk5, 1nk6, 1nk7, 1nk8, 1nk9, 1nkb, 1nkc, 1nke, 1l3s, 2bdp, 4bdp - GsDpo I fragment + DNA

3ht3, 1u45, 1u47, 1u48, 1u49, 1u4b, 1l3t, 1l3u, 1l3v, 1l5u, 1lv5, 3bdp - GsDpo I fragment + DNA + nucleotide

3ikm - hDpo γ1+γ2 - human

3ikl, 2g4c - hDpo γ2

3g6v, 3g6x, 3g6y - hDpo ι + DNA

3gdx - hDpo β + DNA

Family B – 3’-5’ exonuclease activity
1ih7 – EpDpo - Enterobacteria phage RB69

3cfo – EpDpo (mutant)

1waf, 1waj - EpDpo + nucleotide

3nci, 3lds, 3l8b, 3cq8,3cfp, 3cfr, 3kd1, 3kd5 - EpDpo (mutant) + DNA

3ndk, 3ne6, 3ngi, 3nhg, 3nae, 3lzj, 3lzi, 2ozs, 2p5g, 2dy4, 1q9x, 1q9y, 1ig9 - EpDpo (mutant) + DNA + nucleotide

1clq - EpDpo + DNA + nucleotide

2oyq, 2ozm, 2p5o, 2dtu - EpDpo (mutant) + DNA + nucleotide analog

2atq – EpDpo + GP32

1noy – T4Dpo + DNA - Enterobacteria phage T4

1noz – T4Dpo residues 1-388

2ex3 – Dpo (mutant) + DNA terminal protein – Bacillus phage φ29

2py5, 2pzs, 1xhz, 1xi1 – BpDpo (mutant) + DNA

2pyj, 2pyl - BpDpo (mutant) + DNA + nucleotide

1xhx - BpDpo (mutant)

2keb - hDpo αB - NMR

1n5g, 1k0p, 1k18 - hDpo α zinc finger domain- NMR

1zqj – hDpo β + DNA

3e0j - hDpo δ2+δ3

3mr4, 3mr2, 3mr3, 3mr5, 3mr6 - hDpo ε catalytic core + DNA + nucleotide

3oiq - yDpo α + cell division control protein 13 – yeast

3flo - yDpo α subunits A,B

3iay - yDpo δ catalytic subunit + DNA

3oha, 3ohb, 3mfh - yDpo ε (mutant) + DNA

3mfi - yDpo ε (mutant) + DNA + nucleotide

2r8j, 2r8k - yDpo ε catalytic domain + DNA + nucleotide

2xgp, 2xgq, 2wtf - yDpo ε + DNA

3maq, 3k57, 3k58, 3k59, 3k5l, 3k5m - EcDpo II (mutant) + DNA + nucleotide

3k5n - EcDpo II (mutant) + DNA

3k5o, 1q8i - EcDpo II (mutant)

3a2f - PfDpo + PCNA - Pyrococcus furiosus

2jgu - PfDpo

1tgo - TgDpo – Thermococcus gorgonarius

2vwj – TgDpo (mutant) + DNA

2vwk - TgDpo (mutant)

2xhb - Dpo (mutant) + DNA + Thermococcus gorgonarius

1wn7, 1wns – Dpo B - Thermococcus kodakarensis

1qht - Dpo (mutant) – Thermococcus

1d5a – DeDpo – Desulfurococcus

Family C – bacterial chromosomal replicative Dpo
2hnh, 2hqa - EcDpo III subunit α catalytic fragment

2gui – EcDpo III subunit ε N-terminal

1j53, 1j54 - EcDpo III subunit ε N-terminal exonuclease domain

2ido - EcDpo III subunit ε + HOT protein

1ok7 - EcDpo III + EcDpo IV C-terminal

1mmi, 2pol - EcDpo III subunit β

2xur, 3f1v - EcDpo III subunit β (mutant)

3d1e - EcDpo III subunit β + EcDpo II C-terminal

1unn - EcDpo III subunit β + EcDpo IV little finger

3d1g - EcDpo III subunit β + inhibitor

3bep - EcDpo III subunit β + DNA

1njf, 1njg - EcDpo III subunit γ N-terminal domains 1-2

1jqj, 1jql - EcDpo III subunit β, δ(mutant)

1a5t - EcDpo III subunit δ’

1xxh, 1jr3 - EcDpo III subunit γ, δ, δ'

1xxi - EcDpo III subunit γ, δ, δ' + nucleotide

3glh - EcDpo III subunit δ, δ', τ

3glf - EcDpo III subunit δ, δ', τ DNA

3gli - EcDpo III subunit δ, δ', τ, ξ DNA

3glg - EcDpo III subunit δ, δ', τ mutant DNA

2axd, 2ae9, 1du2 - EcDpo III subunit θ - NMR

2aya - EcDpo III subunit τ

1em8 - EcDpo III subunit φ, χ

1bgx – TaDpo + TP7 MAB

Family X – eukaryotic Dpo involved in base excision repair, non-homologous end-joining and V(D)J recombination.
3q8p, 3q8q, 3lk9, 3mby, 3isb, 3isc, 1zjm, 1tv9, 1tva, 1bpx, 1bpz, 1zqa, 1zqb, 1zqc, 1zqd, 1zqf, 1zqg, 1zqh, 1zqi, 1zaj, 1zqk, 1zql, 1zqm, 1zqn, 1zqo, 1zqp, 1zqq, 1zqr, 1zqs, 1zqt, 1zqu, 1zqv, 1zqw, 1zqx, 1zqy, 1zqz, 7ice, 7icf, 7ici, 7icj, 7icl, 7icm, 7icp, 7icr, 7ict, 7icu, 7icv, 8icb, 8icc, 9icj, 9ick, 9icl, 9icm, 9icp, 9icw, 9icx, 9icy, 7icg, 7ich, 7ick, 7icn, 7ico, 7icq, 7ics, 1zqe - hDpo β + DNA

3jpn, 3jpo, 3jpp, 3jpq, 3jpr, 3jpt, 3jps, 3isd, 3c2k, 3c2l, 3c2m, 2pxi, 2iso, 2isp, 2i9g, 2fmp, 2fmq, 2fms, 1zjn, 1mq2, 1mq3, 1bpy, 8ica, 8ice, 8icf, 8icg, 8ich, 8ici, 8icj, 8ick, 8icl, 8icm, 8icn, 8ico, 8icp, 8icq, 8icr, 8ics, 8ict, 8icu, 8icv, 8icw, 8icx, 8icz, 9ice, 9icg, 9ich, 9ici, 9icq, 9ics, 9ict, 9icu, 9icv, 9icr, 9icn, 9ico, 8icy, 9ica, 9icb, 9icc, 9icf - hDpo β + DNA + nucleotide

2p66 - hDpo β + DNA + nucleotide analog

3ogu - hDpo β (mutant) + DNA

2v6z - hDpo β N-terminal (mutant) - NMR

3k75, 3lqc - hDpo β + DNA repair protein XRCC1

2jw5 - hDpo λ BRCT domain

1xsl - hDpo λ catalytic domain

1nzp - hDpo λ lyase domain - NMR

3pmn, 3pnc, 3mda, 2gws, 2bcq, 2bcr, 2bcs, 2bcu, 2bcv, 1xsp, 1rzt - hDpo λ + DNA 3mgh, 3c5f, 3c5g, 2pfn - hDpo λ (mutant) + DNA

3pml, 3mdc, 1xsn - hDpo λ + DNA + nucleotide

3mgi, 3hw8, 3hwt, 3hx0, 2pfo, 2pfp, 2pfq - hDpo λ (mutant) + DNA + nucleotide

2htf, 2dun - hDpo μ BRCT domain – NMR

2ihm - mDpo μ catalytic domain + DNA – mouse

1rpl, 2bpc, 1bpe, 1bpb, 1bpd - rDpo β – rat

2van, 1jn3 - rDpo β (mutant)

1dk2, 1dk3, 1bno, 1bnp - rDpo β N-terminal – NMR

1nom - rDpo β C-terminal

1huo, 1huz - rDpo β + DNA

1bpe - rDpo β + nucleotide

2bpf, 2bpg - rDpo β + DNA + nucleotide

1jms – mTdT

1kej – mTdT+ nucleotide

1kdh - mTdT+ nucleotide + DNA

2w9m – Dpo X – Deinococcus radiodurans

Family Y – translesion Dpo
2i5o - hDpo η ubiquitin-binding zinc finger - NMR

3abd, 3abe - hDpo ξ catalytic subunit Rev3 + mitotic spindle assembly checkpoint protein Rev7

3gqc – hRev1 + DNA + nucleotide

2ebw – hRev1 BRCT domain – NMR

3bjy, 2aq4 – yRev1 catalytic domain + DNA + nucleotide

3q8r, 3q8s, 3h4b, 3h4d, 3gv5, 3gv7, 3gv8, 3epg, 3epi, 2fll, 2fln, 2flp, 2dpi, 2dpj, 2alz, 1zet, 1t3n - hDpo τ + DNA + nucleotide

3ngd, 3osn - hDpo τ catalytic fragment + DNA

3h40 - hDpo τ DNA binding domain + DNA

2ktf - hDpo τ + ubiquitin

2l0f, 2l0g - hDpo τ + ubiquitin – NMR

1t94 - hDpo κ

3in5 - hDpo κ + DNA

2w7o, 2w7p, 2oh2 - hDpo κ + DNA + nucleotide

2kwu, 2kwv - mDpo τ C-terminal + ubiquitin - NMR

3ai4 - mDpo τ/yEGFP

1jih – yDpo η catalytic domain

2rdi - SsDpo IV - Sulfolobus solfataricus

3pr4, 3pr5, 2r8g, 2r8h, 2r8i, 2uvr, 2uvu, 2uvv, 2uvw - SsDpo IV (mutant) + DNA + nucleotide

2xc9, 3m9m, 3m9n, 3m9o, 2v4q, 2v4r, 2ago, 1ryr, 1rys, 2w9a, 2w9b, 2w9c, 3gii, 3gij, 3gik, 3gil, 3gim, 3qz7, 3qz8 - SsDpo IV + DNA

2xca, 2xcp, 3khg, 3khh, 3khl, 3khr, 2w8k, 2w8l, 2rdj, 2v9w, 2va2, 2va3, 2ia6, 2ibk, 2jef, 2jeg, 2jei, 2jej, 2imw, 2j6s, 2j6t, 2j6u, 2asd, 2asj, 2asl, 2atl, 2au0, 2c22, 2c28, 2c2d, 2c2e, 2c2r, 2agp, 2agq, 2bqr, 2bqu, 2br0, 2bq3, 1s9f, 1s97, 1s0m, 1s0n, 1s0o, 1s10, 1n48, 1n56, 1jx4, 1jxl - SsDpo IV + DNA + nucleotide

3fds – SsDpo IV + PCNA B + PCNA C

3bq2 – SaDpo IV + DNA – Sulfolobus acidocaldarius

3bq1 - SaDpo IV + DNA + nucleotide

3bq0 - SaDpo IV + DNA

Prokaryotic Pol I – DNA repair
1s5j – SsDpo I

3eyz - BsDpo I (mutant) + DNA - Bacillus stearothermophilus

3ez5 - BsDpo I (mutant) + DNA + nucleotide

Prokaryotic Pol II – DNA repair
3o59 - PhDpo II large subunit - Pyrococcus horikoshii

2kxe - PhDpo II small subunit

1qqc – DeDpo II

Prokaryotic Pol III – DNA elongation and proofreading
2hpi, 2hpm - TaDpo III α subunit

3e0d - TaDpo III α subunit + DNA

3f2b, 3f2c, 3f2d – Dpo III α subunit + DNA + nucleotide – Geobacillus kaustophilus

1zd7, 1zde, 3nzm - Dpo III α subunit – Synechocystis

2avt - Dpo III β subunit – Streptococcus pyogenes

2awa - Dpo III β subunit – Streptococcus pneumoniae

2p1j – TmDpo III exonuclease domain – Thermotoga maritima

1vpk - TmDpo III β subunit

2gno - TmDpo III γ subunit

2keq - Dpo III α subunit – Nostoc punctiforme

3d1f - EcDpo III β subunit + polypeptide